here's a copy/pasting from one of my post in another thread, hope it'll help :
I made team color this way :
first I erase the part I want team color in Gimp. Then I use nifviewer too put team color instead of transparency.
find a file named TeamColor.bmp in civ4 folders
open the nif of the unit. the part of the skin you have deleted are transparent.
select the unit shape and view it's properties
scroll down and click on NiProperties
double-click on NiTexturingProperties
there you should see base map pointing to the dds skin of the unit.
add a new map (decal) with the same dds, and same properties as base map.
change base map to point to TeamColor.bmp
now you should see no transparency on the model, but a red color on this part instead
save the nif, done.